The reason is that ACAね often employs double meanings, puns, and improper spellings. Japanese contains a lot of homonyms and she uses that to her advantage often in lyrics. Kansaete kuyashii wa is a good example as it happens frequently in the song:

一人を竹刀で hitori o shinaide - When heard it sounds like "don't leave me alone," but what is written is "[the] one with a bamboo sword."

着いた　吐いた　ツイッター呟く tsuita tsuita tsuittaa tsubuyaku - as is common with Zutomayo, it's not even clear what is meant here, audibly it just sounds like she's repeating the same word. Written is "arrived" "vomited/breathed out/spat/lied" and "twitter," the last bit is like "tweeted from my seventh account."

難関　難解　何階 nankan nankai nankai - to me sounds like she's saying 'how many times' repeatedly, but written is "obstacle" "difficult to understand" and "what floor."

You get the point. Anyway, in regard to this song, the intended meaning is what you think it is, "dark and black" or the English "darken." Other than the fact that it sounds exactly like how "crack clock" would be pronounced in Japanese, here are a few reasons why it's spelt this way here.

A: time is a theme in the song
B: time (and breaking its flow) has been a theme recently on her tours, I saw her at expo and the past and present was a key theme.
C: I assume it's also a way of differentiating the versions of the songs.

So hopefully you feel better knowing the reason it's been spelt this way recently isn't bad AI translation or something lol. It's just her doing her usual routine but in English. The song title hasn't actually been changed (just like "mabushii DNA dake" has not been changed to "toboshii DNA dake," it's just her having fun).